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Improved structure of mouse Gasdermin D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6N9N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293.15 27%PEG3350, 0.1M Bis-Tris
Crystal Properties Matthews coefficient Solvent content 2.42 49.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.209 α = 90 b = 86.934 β = 95.24 c = 82.466 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2023-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98011 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.636 82.121 92.3 0.056 0.999 11.3 11.4 16610
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.636 2.958 68.7 0.679 12
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.636 33.95 16596 781 59.1 0.2396 0.2386 0.2372 0.2595 0.2741 RANDOM 89.75
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.9516 -9.5483 3.6975 -1.7459
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.32 t_omega_torsion 2.25 t_angle_deg 0.88 t_bond_d 0.006 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6158 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 17
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction autoPROC data scaling MOLREP phasing